An adaptive and modular framework for evolving deep neural networks

Santos, F. J. J. B., Gonçalves, I., & Castelli, M. (2023). Neuroevolution with box mutation: An adaptive and modular framework for evolving deep neural networks. Applied Soft Computing, 147(November), 1-15. [110767]. https://doi.org/10.1016/j.asoc.2023.110767 --- Funding: This work is funded by national funds through the FCT - Foundation for Science and Technology, I.P., within the scope of the projects CISUC - UID/CEC/00326/2020, UIDB/04152/2020 - Centro de Investigação em Gestão de Informação (MagIC)/NOVA IMS, and by European Social Fund, through the Regional Operational Program Centro 2020 .The pursuit of self-evolving neural networks has driven the emerging field of Evolutionary Deep Learning, which combines the strengths of Deep Learning and Evolutionary Computation. This work presents a novel method for evolving deep neural networks by adapting the principles of Geometric Semantic Genetic Programming, a subfield of Genetic Programming, and Semantic Learning Machine. Our approach integrates evolution seamlessly through natural selection with the optimization power of backpropagation in deep learning, enabling the incremental growth of neural networks’ neurons across generations. By evolving neural networks that achieve nearly 89% accuracy on the CIFAR-10 dataset with relatively few parameters, our method demonstrates remarkable efficiency, evolving in GPU minutes compared to the field standard of GPU days.publishersversionpublishe

NONLINEAR VIBRATIONS OF FLUID-FILLED VISCOELASTIC CYLINDRICAL SHELLS

In this work the non-linear vibrations of a simply supported viscoelastic fluid-filled circular cylindrical shells subjected to lateral harmonic load is studied. Donnell's non-linear shallow shell theory is used to model the shell, assumed to be made of a Kelvin-Voigt material type, and a modal solution with six degrees of freedom is used to describe the lateral displacements. The Galerkin method is applied to derive a set of coupled non-linear ordinary differential equations of motion. The influence of shell geometry, flow velocity and dissipation parameter are studied and special attention is given to resonance curves. Obtained results show that the viscoelastic dissipation parameter, flow velocity and geometry have significant influence on the nonlinear behavior of the shells as displayed in instability loads and resonance curves

Influence of seagrass meadows on nursery and fish provisioning ecosystem services delivered by Ria Formosa, a coastal lagoon in Portugal

This study is the first to evaluate the fish provisioning services of a whole transitional landscape (Ria Formosa lagoon, Portugal), in parallel with the enhancement of growth, survival and production of single cohorts of the most important commercial fish species by vegetated and unvegetated sub-tidal habitats. Based on monthly beach seine samples, total density and biomass of 96 species of fishes were 1.89 and 3.03 times greater in vegetated habitats than unvegetated habitats, respectively. Vegetated habitat enhanced survival in six of eight commercial species for which survival could be estimated in both habitats. The total production of all 12 commercially important species within vegetated habitat was approximately double that of unvegetated habitat, with production enhancement in 7 of 12 species ranging from 1.8 to 169-fold for the vegetated habitats. Within the lagoon, vegetated sub-tidal habitat covers an area 5-fold smaller than unvegetated habitat, yet it accounts for 27.1 % of fish production. Estimated total lifetime economic values of the single cohorts of the 12 commercial species were between 30 million and 59 million EUR. An exceptionally strong year class of the European seabass (Dicentrarchus labrax), a species with higher density and biomass in unvegetated habitat, accounts for the higher overall values per hectare for unvegetated habitat (Low natural mortality (M): EUR 32,844 ha-1; High M: EUR 16,751 ha-1) than for vegetated habitat (Low M: EUR 22,028 ha-1; High M: EUR 10,700 ha-1). These results highlight the enormous importance of temperate coastal lagoons as a nursery and source of recruits for coastal fisheries. Our evaluation of fish provisioning services based on data for individual cohorts of fish for a whole transitional landscape is a stronger and more valid approach for estimating future biomass and value than previous studies based on mean densities and biomasses of fish that did not distinguish between cohorts.ICTIORIA (Recruitment of sea breams) DG XIV C1/99/061; LA/P/0101/2020;info:eu-repo/semantics/publishedVersio

Wild dogs at stake: deforestation threatens the only Amazon endemic canid, the short-eared dog (Atelocynus microtis)

The persistent high deforestation rate and fragmentation of the Amazon forests are the main threats to their biodiversity. To anticipate and mitigate these threats, it is important to understand and predict how species respond to the rapidly changing landscape. The short-eared dog Atelocynus microtis is the only Amazon-endemic canid and one of the most understudied wild dogs worldwide. We investigated short-eared dog habitat associations on two spatial scales. First, we used the largest record database ever compiled for short-eared dogs in combination with species distribution models to map species habitat suitability, estimate its distribution range and predict shifts in species distribution in response to predicted deforestation across the entire Amazon (regional scale). Second, we used systematic camera trap surveys and occupancy models to investigate how forest cover and forest fragmentation affect the space use of this species in the Southern Brazilian Amazon (local scale). Species distribution models suggested that the short-eared dog potentially occurs over an extensive and continuous area, through most of the Amazon region south of the Amazon River. However, approximately 30% of the short-eared dog's current distribution is expected to be lost or suffer sharp declines in habitat suitability by 2027 (within three generations) due to forest loss. This proportion might reach 40% of the species distribution in unprotected areas and exceed 60% in some interfluves (i.e. portions of land separated by large rivers) of the Amazon basin. Our local-scale analysis indicated that the presence of forest positively affected short-eared dog space use, while the density of forest edges had a negative effect. Beyond shedding light on the ecology of the short-eared dog and refining its distribution range, our results stress that forest loss poses a serious threat to the conservation of the species in a short time frame. Hence, we propose a re-assessment of the short-eared dog's current IUCN Red List status (Near Threatened) based on findings presented here. Our study exemplifies how data can be integrated across sources and modelling procedures to improve our knowledge of relatively understudied species

Rabbit derived VL single-domains as promising scaffolds to generate antibody–drug conjugates

© The Author(s) 2023. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.Antibody-drug conjugates (ADCs) are among the fastest-growing classes of therapeutics in oncology. Although ADCs are in the spotlight, they still present significant engineering challenges. Therefore, there is an urgent need to develop more stable and effective ADCs. Most rabbit light chains have an extra disulfide bridge, that links the variable and constant domains, between Cys80 and Cys171, which is not found in the human or mouse. Thus, to develop a new generation of ADCs, we explored the potential of rabbit-derived VL-single-domain antibody scaffolds (sdAbs) to selectively conjugate a payload to Cys80. Hence, a rabbit sdAb library directed towards canine non-Hodgkin lymphoma (cNHL) was subjected to in vitro and in vivo phage display. This allowed the identification of several highly specific VL-sdAbs, including C5, which specifically target cNHL cells in vitro and present promising in vivo tumor uptake. C5 was selected for SN-38 site-selective payload conjugation through its exposed free Cys80 to generate a stable and homogenous C5-DAB-SN-38. C5-DAB-SN-38 exhibited potent cytotoxicity activity against cNHL cells while inhibiting DNA-TopoI activity. Overall, our strategy validates a platform to develop a novel class of ADCs that combines the benefits of rabbit VL-sdAb scaffolds and the canine lymphoma model as a powerful framework for clinically translation of novel therapeutics for cancer.This work was supported by the Portuguese Funding Agency, Fundação para a Ciência e Tecnologia, FCT IP (SAICT/2017/32085, PTDC/QUI-OUT/3989/2021 and Ph.D. fellowship SFRH/BD/131468/2017 to ASA and SFRH/BD/90514/2012 to JD). CIISA has provided support through Project UIDB/00276/2020, funded by FCT and LA/P/0059/2020-AL4AnimalS. Research Institute for Medicines (iMed.ULisboa) acknowledges the financial support of Fundação para a Ciência e Tecnologia (Projects: PTDC/QUI-OUT/3989/2021; UIDB/04138/2020 and UIDP/04138/2020). The NMR spectrometers are part of the National NMR Network (PTNMR) and are partially supported by Infrastructure Project Nº 022161 (co-financed by FEDER through COMPETE 2020, POCI and PORL and FCT through PIDDAC).info:eu-repo/semantics/publishedVersio

Clay content drives carbon stocks in soils under a plantation of Eucalyptus saligna Labill. in southern Brazil

Soil carbon accumulation is largely dependent on net primary productivity. To our knowledge, there have been no studies investigating the dynamics of carbon accumulation in weathered subtropical soils, especially in managed eucalyptus plantations. We quantified the seasonal input of leaf litter, the leaf decomposition rate and soil carbon stocks in an commercial plantation of Eucalyptus saligna Labill. in southern Brazil. Our goal was to evaluate, through multiple linear regression, the influence that certain chemical characteristics of litter, as well as chemical and physical characteristics of soil, have on carbon accumulation in soil organic matter fractions. Variables related to the chemical composition of litter were not associated with the soil carbon stock in the particulate and mineral fractions. However, certain soil characteristics were significantly associated with the carbon stock in both fractions. The concentrations of nutrients associated with plant growth and productivity, such as phosphorus, sulfur, copper and zinc, were associated with variations in the labile carbon pool (particulate fraction). Clay content was strongly associated with the carbon stock in the mineral fraction. The carbon accumulation and stabilization in weathered subtropical Ultisol seems to be mainly associated with the intrinsic characteristics of the soil, particularly clay content, rather than with the quantity, chemical composition or decomposition rate of the litter

A revision of the status of Lepadogaster lepadogaster (Teleostei : Gobiesocidae): sympatric subspecies or a long misunderstood blend of species?

Molecular (partial mitochondrial 12S ribosomal DNA sequences), morphological and meristic analysis of Lepadogaster lepadogaster lepadogaster, L. l. purpurea and L. zebrina were performed to investigate the relationships between these taxa. On the western shore of mainland Portugal, where the two subspecies of L. lepadogaster occur sympatrically, they differ in microhabitat preferences and their breeding seasons are largely out of phase. This information, combined with data on distribution patterns, led to the following conclusions: Lepadogaster l. purpurea is considered to be a valid species, L. purpurea (Bonnaterre, 1788), different from L. l. lepadogaster, now designated L. lepadogaster (Bonnaterre, 1788). L. zebrina was found to be a synonym of L. lepadogaster. The two newly defined species were found to be in sympatry at Madeira and the Canary islands, the Atlantic coast of the Iberian Peninsula, and the Mediterranean at least as far as Genoa (Italy). Diagnostic characters and a list of synonyms are provided. (C) 2002 The Linnean Society of London, Biological Journal of the Linnean Society, 2002, 76, 327-338

Corrigendum to 'Editor's Choice - European Society for Vascular Surgery (ESVS) 2020 Clinical Practice Guidelines on the Management of Vascular Graft and Endograft Infections' [European Journal of Vascular & Endovascular Surgery 59/3 (2020) 339-384]

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